SHRiMP2: Sensitive yet practical short read mapping

Bioinformatics

Volumn 27, Issue 7, 2011, Pages 1011-1012

  David, Matei ^a   Dzamba, Misko ^b   Lister, Dan ^b   Ilie, Lucian ^c   Brudno, Michael ^b,d  

^a Princeton University   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF WESTERN ONTARIO   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DECAPODA (CRUSTACEA);

ALGORITHM; ARTICLE; CHROMOSOME MAP; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC POLYMORPHISM; GENOMICS; METHODOLOGY; SEQUENCE ALIGNMENT;

ALGORITHMS; CHROMOSOME MAPPING; GENOMICS; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 79953310937     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr046     Document Type: Article

References (9)

1. Homer, N. et al. (2009) Bfast: an alignment tool for large scale genome resequencing. PLoS ONE, 4, e7767.
2. Ilie, L. and Ilie, S. (2007) Multiple spaced seeds for homology search. Bioinformatics, 23, 2969-2977.
3. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biol., 10, R25.
4. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
5. Li, H. and Homer, N. (2010) A survey of sequence alignment algorithms for nextgeneration sequencing. Brief. Bioinform., 11, 473-483.
6. Rasmussen, K.R. et al. (2006) Efficient q-gram filters for finding all e-matches over a given length. J. Computat. Biol., 13, 296-308.
7. Rumble, S.M. et al. (2009) Shrimp: accurate mapping of short color-space reads. PLoS Comput. Biol., 5, e1000386.
8. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
9. Wu, T.D. and Nacu, S. (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26, 873-881.